#------------------- FETCH (10/ 1/09) --------------------------
# Note: This menu requires that the shell script 'GBfilter' be
# in your bin directory.
item:FETCH
itemmethod: $NAMES; (fetch $WHATTOGET $DATABASE in1.nam in1.tmp; rm in1.nam; $WHERE) &
itemhelp:doc/xylem/fetch.txt
itemopen:gde_help_viewer.csh

arg:NAMES
arglabel:NAMES/ACCESSION #'S
argtype:chooser
argchoice:Single name/acc:echo $IDNUM > in1.nam
argchoice:Create list of names/acc#'s:cat $DOC/xylem/GDE/namefile.template > in1.tmpname; $GDE_TEXTEDIT in1.tmpname; egrep -v -e \; in1.tmpname >in1.nam;rm in1.tmpname* 
argchoice:File of Names/Acc.#'s:cat $NAMEFILE >in1.nam
argvalue:0

arg:IDNUM
arglabel:Single name or accession #
argtype:text

arg:NAMEFILE
arglabel:File of names/acc. #'s
argtype:text
#@argtype:file_chooser

arg:WHATTOGET
arglabel:WHAT TO GET
argtype:chooser
argchoice:annotation:-a
argchoice:sequence:-s
argchoice:both:-b
argvalue:2

arg:DATABASE
arglabel:DATABASE
argtype:chooser
argchoice:GenBank:-g
argchoice:GenBank Dataset:-G $DBFILE
argchoice:PIR:-p
argchoice:PIR Dataset:-P $DBFILE
argvalue:0

arg:DBFILE
arglabel:Dataset
argtype:text

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
argchoice:GDE:(GBfilter in1.tmp in1.gen; gde in1.gen; rm in1.*)&
argchoice:Textedit window:($GDE_TEXTEDIT in1.tmp;rm in1.tmp) &
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' Fetch completed'
argchoice:GenBank Dataset:splitdb -g in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
argchoice:PIR Dataset:splitdb -p in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
argvalue:0

arg:OUTFILE
arglabel:Output file or Dataset name
argtype:text

in:in1
informat:genbank